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Update CaImAn utilities for compatibility with latest CaImAn #113

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merged 4 commits into from
Jun 5, 2024
Merged

Update CaImAn utilities for compatibility with latest CaImAn #113

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647142f
Update(run_caiman.py) logic to handle caiman output files
kushalbakshi Jun 5, 2024
12a79de
Run shutil with full path
kushalbakshi Jun 5, 2024
f78acfc
Copy files instead of move out of temp_dir
kushalbakshi Jun 5, 2024
843ac6d
Fix(caiman_loader.py): pass generator obj as list to np.dstack
kushalbakshi Jun 5, 2024
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6 changes: 4 additions & 2 deletions element_interface/caiman_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -293,8 +293,10 @@ def _get_image(self, img_type):
)
else:
img_ = np.dstack(
pln_cm.motion_correction[img_type][...]
for pln_cm in self.planes.values()
[
pln_cm.motion_correction[img_type][...]
for pln_cm in self.planes.values()
]
)
return img_

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12 changes: 9 additions & 3 deletions element_interface/run_caiman.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import pathlib

import cv2
import os
import pathlib
import shutil

try:
cv2.setNumThreads(0)
Expand Down Expand Up @@ -65,6 +66,11 @@ def run_caiman(

cnmf_output_file = pathlib.Path(cnmf_output.mmap_file[:-4] + "hdf5")
assert cnmf_output_file.exists()
assert cnmf_output_file.parent == pathlib.Path(output_dir)
output_files = os.listdir(cnmf_output_file.parent)
for output_file in output_files:
try:
shutil.copy(cnmf_output_file.parent / output_file, output_dir)
except FileExistsError:
print(f"File {output_file.name} already exists in {output_dir}. Skipping.")

_save_mc(mc_output, cnmf_output_file.as_posix(), parameters["is3D"])
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